ABSTRACT Cryptophytes are a ubiquitous algal group and are important primary producers in aquatic ecosystems. Identification of lineages within the group is difficult because of their simple morphology and they are often enumerated at the class level in ecological research. Despite the increasing number of molecular probes used for identification of microorganisms, rRNA genes (i.e. nuclear 18S, ITS, and 28S, and nucleomorph 18S) are the markers most commonly used to identify cryptophytes. To provide a broader choice of markers, we compared and characterised the utility of 13 plastid genes in 23 culture strains, which cover the spectrum cryptophycean lineages (Clades 1–5). The genes include 11 protein-coding (atpA, atpB, chlI, clpC, dnaK, psaA, psbA, rbcL, rpoC1, secA, and tufA) and two ribosomal RNA (plastid 16S and 23S) genes. Most of the genes were successfully amplified and sequenced using newly designed primers, and the sequences aligned with minimal indels. The protein-coding genes showed higher levels of divergence (P-distance, and synonymous and nonsynonymous substitution rates) and higher identification index than those of rRNAs. Considering divergence and phylogenetic usefulness, we selected atpB, psaA, and rbcL as the best candidates for cryptophycean clade identification and further field research.

中文翻译：

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质体编码的基因比较揭示了 atpB、psaA 和 rbcL 在鉴定含质体隐植物进化枝和系统发育方面的有用性

摘要 隐藻是一种普遍存在的藻类，是水生生态系统中重要的初级生产者。群体内的谱系因其形态简单而难以识别，并且在生态研究中经常在类级别进行列举。尽管用于鉴定微生物的分子探针数量不断增加，但 rRNA 基因（即核 18S、ITS 和 28S 以及核型 18S）是最常用于鉴定隐生植物的标记。为了提供更广泛的标记选择，我们比较并表征了 23 个培养菌株中 13 个质体基因的效用，这些菌株涵盖了隐藻谱系（进化枝 1-5）。这些基因包括 11 个蛋白质编码（atpA、atpB、chlI、clpC、dnaK、psaA、psbA、rbcL、rpoC1、secA 和 tufA）和两个核糖体 RNA（质体 16S 和 23S）基因。大多数基因使用新设计的引物成功扩增和测序，序列与最少的插入缺失对齐。与 rRNA 相比，蛋白质编码基因显示出更高水平的差异（P 距离、同义和非同义替换率）和更高的识别指数。考虑到分歧和系统发育的有用性，我们选择了 atpB、psaA 和 rbcL 作为密码学进化枝识别和进一步实地研究的最佳候选者。